Very useful tool! I have tried it on my own dataset, and it seems to work very well. I have noticed one small thing though: concave shapes are not always rendered correctly (example from the Delft dataset: https://imgur.com/a/eBBxA). I would love to contribute and fix it, but unfortunately I am not sufficiently familiar with node.js. If you would be able to have a look at it, could you please let me know?
It should be easy enough to allow passing additional projections from
a command line argument. Unfortunately I currently don't have the time
to implement it. If you do, I will be happy to accept a pull request.
Unfortunately I haven't seen that error message before, and therefore
cannot help you with a solution.
I'm not actively using/maintaining "citygml-to-3dtiles" (it was more
of a personal experiment). I hope you find a way to solve the problem!